Entering edit mode
8.2 years ago
blur
▴
280
Hi,
I have been running Picard-tools markDuplicates for 5 hours now... I get a msg. saying it is traversing - but no output file seemes to be generated. Is it stuck? should I kill it and start again? BTW - my server is seriously over-loaded... might this too be a factor?
Thanks,
Dear blur, Hi
maybe you can use "
ps aux" or :ps aux | grep program-nameProcess state codes:
D uninterruptible sleep (usually IO)
R running or runnable (on run queue)
S interruptible sleep (waiting for an event to complete)
T stopped, either by a job control signal or because it is being traced
W paging (not valid since the 2.6.xx kernel)
X dead (should never be seen)
Z defunct ("zombie") process, terminated but not reaped by its parent
< high-priority (not nice to other users)
N low-priority (nice to other users)
L has pages locked into memory (for real-time and custom IO)
s is a session leader
l is multi-threaded (using CLONE_THREAD, like NPTL pthreads do)
(plus sign +) is in the foreground process group
Hi, I get S ( interruptible sleep ) does that mean it's stuck? or that it would eventually complete?
what's your version of picard ? what's the input ? for WGS this tool can take hours or days.
Hard to say anything concrete. If you look at
topso you see the picard process consuming any CPU?It is running and consuming lots and lots of CPUs... maybe it's just a memory problem?
It is running and consuming lots and lots of CPUs... maybe it's just a memory problem?
Hi,
you can use your Linux "System Monitor" GUI to check your system Memory and Swap consumption.